Mobile elements are important intrinsic contributors to the genetic instability of the human genome. Mechanisms by which they damage DNA involve Alu/Alu recombination, insertional mutagenesis, and the creation of DNA double-strand breaks. Although largely underestimated, Alu/Alu recombination is thought to cause approximately 0.5% of new human genetic diseases, and is almost certainly a significant player with genetic instability in some cancers, such as leukemia. Currently, little is known about what sequence components and genetic background that affect this type of instability, which without this knowledge, understanding the contribution of Alu/Alu to human disease would be limited. The overall objective of this proposal is to characterize the cis and trans factors that influence Alu/Alu recombination in order to predict genomic regions that will be more prone to this type of instability. This is made possible with the use of a unique reporter system that we have developed. Our central hypothesis is that sequence-specific features in, and around, Alu elements influence this recombination process. The rationale for the hypothesis is that only when we clearly identify the factors controlling the rate of Alu/Alu recombination events will we be able to predict and understand their contributions to genetic disease and to cancer. To achieve our objective we have developed the following specific aims: 1) To measure the influence of mismatches, spacing, orientation etc. on recombination between Alus and predict genomic regions of instability. This will answer our hypothesis that sequence-specific factors modify the rate of Alu/Alu recombination and develop a model to predict the contribution of Alu/Alu recombination to genetic instability throughout the genome. 2) To determine the influence of L1-induced DSBs as a DNA damaging agent as a trigger for Alu/Alu recombination. We postulate that L1-induced DSBs contribute to Alu/Alu recombination and can be readily measured using our reporter gene and whole genome paired-end sequencing procedures. 3) To test the influence of DNA repair defects, particularly mismatch repair on the Alu/Alu recombination process. We hypothesize that mismatch-repair-related defects will alter the rate and spectrum of Alu/Alu recombination in the genome and will utilize our reporter system and whole genome sequence studies to test this process and to study other repair defects. These studies are innovative because our new approaches will allow us to address these questions in a way that was not previously feasible in such a global manner. They further the goals of the Public Health Service by helping predict regions of genetic instability in the genome and the role that Alu and L1 elements play in that instability. Our results will have a positive impact by providing information critical for understanding and predicting on a genome-wide basis the individual heterogeneity in these processes that make some individuals and cell types much more prone to diseases based on these forms of instability. PUBLIC HEALTH RELEVANCE: Alu elements are the most abundant repeated sequence in the human genome and therefore contribute regions of homology leading to non-allelic homologous recombination that causes DNA rearrangements leading to many human diseases. In addition, L1 elements cause DNA double-strand breaks that also contribute to these recombination events. We hypothesize that we can devise rules to predict genomic regions subject to this stability and in which diseases they are most likely to contribute. This is highly relevant to public health in that it can help predict individual risk and improve patient diagnostics.